pdbtools: how to set the occupancy for an atom selection?
Hello, I was wondering if someone could show me a way to set the occupancy of a specific set of atoms to 0 using phenix.pdbtools. I noticed here http://www.phenix-online.org/download/documentation/cci_apps/pdbtools.html#a... that there is no option under modify => occupancies to do an 'atom_selection'. Any help would be appreciated. Cheers, Alex
By the way, will you please let me know from which step we have the b-factors in the PDB files? Do the b-factors change with the progression of phenix refinement?
Smith
At 2015-04-13 21:46:20, "Alejandro Virrueta"
Smith, would you mind changing a subject line when changing the topic of conversation? Your question below has a little to do with "pdbtools: how to set the occupancy for an atom selection?".
By the way, will you please let me know from which step we have the b-factors in the PDB files? Do the b-factors change with the progression of phenix refinement?
They may be set to a value or stem from a refinement run. Here is another attempt at convincing you to some reading about basics: http://journals.iucr.org/d/issues/2012/04/00/ba5180/ba5180.pdf Pavel
Hi Alex, There is an option "occupancies.set=0". Hope this helps! Best, Chen On Mon, Apr 13, 2015 at 9:46 AM, Alejandro Virrueta < [email protected]> wrote:
Hello,
I was wondering if someone could show me a way to set the occupancy of a specific set of atoms to 0 using phenix.pdbtools.
I noticed here https://urldefense.proofpoint.com/v2/url?u=http-3A__www.phenix-2Donline.org_download_documentation_cci-5Fapps_pdbtools.html-23anch2&d=AwMFaQ&c=-dg2m7zWuuDZ0MUcV7Sdqw&r=uV9bK9zAIvRZlk7q6-YllA&m=87qSRfQW1CF7Y8dPbUwv6L-pEFJx7zkKKAGsjVS09c0&s=NAHtEINOsS50QpVDKV-8_cB2290WJzzmSscacsNddls&e= that there is no option under modify => occupancies to do an 'atom_selection'. Any help would be appreciated.
Cheers, Alex
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Hi Alex, Phenix GUI -> Model tools -> PDB Tools -> Options -> click on Occupancies -> in popped up window type in atom selection and choose one of three available actions (randomize..., set..., reset...) -> hit OK -> hit Run. I think that should do it. In the command line: phenix.pdbtools model.pdb occupancies.set=0.46 selection="chain A and resseq 1:2" Pavel On 4/13/15 6:46 AM, Alejandro Virrueta wrote:
Hello,
I was wondering if someone could show me a way to set the occupancy of a specific set of atoms to 0 using phenix.pdbtools.
I noticed here http://www.phenix-online.org/download/documentation/cci_apps/pdbtools.html#a... that there is no option under modify => occupancies to do an 'atom_selection'. Any help would be appreciated.
Cheers, Alex
participants (4)
-
Alejandro Virrueta -
Chen Zhao -
Pavel Afonine -
Smith Liu